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# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Turn an mmCIF file into a dictionary."""
from Bio.File import as_handle
class MMCIF2Dict(dict):
"""Parse a mmCIF file and return a dictionary."""
def __init__(self, filename):
"""Parse a mmCIF file and return a dictionary.
Arguments:
- file - name of the PDB file OR an open filehandle
"""
self.quote_chars = ["'", '"']
self.whitespace_chars = [" ", "\t"]
with as_handle(filename) as handle:
loop_flag = False
key = None
tokens = self._tokenize(handle)
try:
token = next(tokens)
except StopIteration:
return # for Python 3.7 and PEP 479
self[token[0:5]] = token[5:]
if not token[0:5].startswith("data_"):
raise ValueError(
"The input mmCIF file must begin with a 'data_' directive."
)
i = 0
n = 0
for token in tokens:
if token.lower() == "loop_":
loop_flag = True
keys = []
i = 0
n = 0
continue
elif loop_flag:
# The second condition checks we are in the first column
# Some mmCIF files (e.g. 4q9r) have values in later columns
# starting with an underscore and we don't want to read
# these as keys
if token.startswith("_") and (n == 0 or i % n == 0):
if i > 0:
loop_flag = False
else:
self[token] = []
keys.append(token)
n += 1
continue
else:
self[keys[i % n]].append(token)
i += 1
continue
if key is None:
key = token
else:
self[key] = [token]
key = None
# Private methods
def _splitline(self, line):
# See https://www.iucr.org/resources/cif/spec/version1.1/cifsyntax for the syntax
in_token = False
# quote character of the currently open quote, or None if no quote open
quote_open_char = None
start_i = 0
for i, c in enumerate(line):
if c in self.whitespace_chars:
if in_token and not quote_open_char:
in_token = False
yield line[start_i:i]
elif c in self.quote_chars:
if not quote_open_char and not in_token:
quote_open_char = c
in_token = True
start_i = i + 1
elif c == quote_open_char and (
i + 1 == len(line) or line[i + 1] in self.whitespace_chars
):
quote_open_char = None
in_token = False
yield line[start_i:i]
elif c == "#" and not in_token:
# Skip comments. "#" is a valid non-comment char inside of a
# quote and inside of an unquoted token (!?!?), so we need to
# check that the current char is not in a token.
return
elif not in_token:
in_token = True
start_i = i
if in_token:
yield line[start_i:]
if quote_open_char:
raise ValueError("Line ended with quote open: " + line)
def _tokenize(self, handle):
empty = True
for line in handle:
empty = False
if line.startswith("#"):
continue
elif line.startswith(";"):
# The spec says that leading whitespace on each line must be
# preserved while trailing whitespace may be stripped. The
# trailing newline must be stripped.
token_buffer = [line[1:].rstrip()]
for line in handle:
line = line.rstrip()
if line.startswith(";"):
yield "\n".join(token_buffer)
line = line[1:]
if line and line[0] not in self.whitespace_chars:
raise ValueError("Missing whitespace")
break
token_buffer.append(line)
else:
raise ValueError("Missing closing semicolon")
yield from self._splitline(line.strip())
if empty:
raise ValueError("Empty file.")
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